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You've got a point morph, but if you think about it like this:
Say you list the 50 or 100 newest freesites on your mainpage, the rest will move on down. So if you have a couple of 1000 freesites linking to you and only link back to 100 of them from your mainpage, and to the rest you link back from your category pages, you still have a lot more in links than outlinks, to your mainpage at least. And plus, the in-links to the freesite from the other linklists make the link back to your linklist weigh more, you wouldn't have that if all LL's used script links
And it would make freesite submission less interesting, say you build a 1000 freesites, and you get a couple se hits on each, that will start to count after a while, and you won't get them if everybody links to the freesite with a script link. If you take that away it would also maybe lead to sooner taking down a freesite by a builder.
Just my $0.02
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